What information goes into the quantitation methods file?

[buijt]

With the release of the new SmartPeak user session feature, I must provide a "quantitation methods" file before I can execute the LCMS_MRM_Unknowns workflow preset. However, I do not quite understand what information should be captured in this file.

From the example datasets, I can infer that the following columns are required:

• "IS_name" this is self-explanatory
• "component_name" also self-explanatory
• "feature_name" the example file fills this with the value "peak_apex_int" so this presumably can specify any SmartPeak meta_value, but I am not quite sure.
• "concentration_units" is self-explanatory
• "transformation_model" "transformation_model_param_slope" and "transformation_model_param_intercept" puzzle me. Where should I expect to derive this information for each component? Does Smartpeak have the capability to compute these values for me?
• The remaining columns "transformation_model_param_x_datum_min" "transformation_model_param_x_datum_max" "transformation_model_param_y_datum_min" and "transformation_model_param_y_datum_max" are filled with placeholder values, but I am not sure how these relate to / affect the transformation model.

I would appreciate if you could explain how I should fill out the quantitation methods file for my data. Thank you!

[dmccloskey]

Thanks for the question. Let me add in a few explanations below:

• "feature_name": this can be either "peak_apex_int" (peak height) or "intensity" (peak area) currently.
• "transformation_model": Currently only linear models are supported at this time. The linear model is of the form y = mx + b where y is the concentration ratio, x is the peak height or area ratio, and m and b are the slop and intercept of the best fit line. Future versions could potentially support more complicated models.
• "transformation_model_param_slope" and "...param_intercept": These can either be calculated by SmartPeak by running Calculate_Quantitation_Methods based on a given set of calibration standards provided in the file StandardsConcentrations.csv. Alternatively, the user can provide these values if they are already known (e.g., at the extreme end if a single point calibration based on a known concentration of internal standard is used).
• "..._min" and "...max": These set the minimum and maximum x and y values to consider when fitting the linear model

Hopefully, some useful references:

• QuantitationMethod class documentation https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/nightly/html/classOpenMS_1_1AbsoluteQuantitation.html#details
• Example for fitting a calibration curve based on user supplied calibration standards https://github.com/AutoFlowResearch/SmartPeak/tree/develop/src/examples/data/LCMS_MRM_Standards

Please let me know if that is helpful (or not).

[buijt]

Thank you for the quick response. I will look into this.